sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
a64c8319996b7ababebb7e8cdc9771c8e91c491b260fd814a035349e9d8fe554 | Python | 10,034 | 200 |
# TODO: standardize on `def lookup_{key}(): return overrides[key]`?
from .utils import PheWebError, load_module_from_filepath
from . import parse_utils
import os, boltons.fileutils
from typing import Optional,Any,Dict,Tuple,List
# All state lives in this dictionary.
# PheWeb should run fine when this is empty.
# M... |
f158b274d37eaadcd3b0124c61d8a2211f504f785aacc57afdc17e892233a5b3 | Python | 10,037 | 320 | # Copyright 2018-2024 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
97bb39b29db08eeb6f7e0021e6502d00dc4f967fc8c8e029f853d06dbd4dd5b3 | Python | 10,039 | 269 | """Modules to extract stimulus features."""
import numpy as np
import torch
from typing import List
from transformers import AutoConfig, AutoModel, AutoTokenizer
from DataSequence import DataSequence
from hard_coded_things import (
bad_words,
bad_words_with_sentence_boundaries,
sentence_end_word,
sent... |
193fdb1e57d7793678a2c2989cb442f985606ba11adb7f98aac30e10e798ce35 | Python | 10,040 | 255 | # Copyright 2025 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agre... |
ee8475b2ee654458bbb3649b1e3bc214cb54878bd8b61b233ea8981815a89243 | Python | 10,042 | 218 | '''
Script to visualize the planning benchmark results stored in a hdf5 database.
'''
#----------------------------------------------------------
# default values
database_name_default = 'build/planning_results.hdf5'
#----------------------------------------------------------
import argparse
import h5py
import matplo... |
8b61ddcc85e41a6125bce25a1e2644e9101324fd20fefa230094ef3a9a720bf1 | Python | 10,058 | 184 | import os
import argparse
import random
import torch
import numpy as np
import logging
from warnings import simplefilter
from scipy.sparse import SparseEfficiencyWarning
from manager.trainer import Trainer
from manager.evaluator import Evaluator_multiclass, Evaluator_multilabel
from model.Classifier_model import Classi... |
f461bfe6788f63d6db1cbc821efb01f67b8c536fe208b6b1ee42f849e0509456 | Python | 10,067 | 369 | from __future__ import annotations
from typing import (
TYPE_CHECKING,
cast,
)
from pandas._libs import (
NaT,
lib,
)
from pandas.errors import InvalidIndexError
from pandas.core.dtypes.cast import find_common_type
from pandas.core.algorithms import safe_sort
from pandas.core.indexes.base import (
... |
24cc0d9a94717e403720243a4f36a3f36e6a59f4f0ea3a4702f50ad76a5fdb81 | Python | 10,073 | 301 | #! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this wo... |
50b9e5a868f0dcf80e2022d6a6c524465c7db36bd83a2ddf5e660bb1405db72a | Python | 10,088 | 286 | # MOFTransformer version 2.0.0
import os
import random
import json
import pickle
import numpy as np
import torch
from torch.nn.functional import interpolate
class Dataset(torch.utils.data.Dataset):
def __init__(
self,
data_dir: str,
split: str,
nbr_fea_len: int,
... |
25bab5d58442e9cd819b19162457762d12c1360eaace555925a494ae3f04578b | Python | 10,089 | 279 | """Process TFC data."""
from pathlib import Path
import numpy as np
import pandas as pd
from .fp_data import debleach_signals, fit_linear, save_data, trial_normalize
def make_tfc_comp_times(
n_trials: int, baseline: int, cs_dur: int, trace_dur: int, us_dur: int, iti_dur: int
) -> pd.DataFrame:
"""
Crea... |
022db47835447a99c25f0530e2320a633de7db60383b60bb7a7aad7a65c0dbba | Python | 10,092 | 332 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
5fda30a8df1f39f52ea04a7a4352bc3bedd4683241f01922f3badcdaf4ec4d02 | Python | 10,094 | 278 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
421c6a209ca1b90f418b8e1bb6666c32cdfd841671e7fea70510352afdcc83cc | Python | 10,096 | 250 | # Copyright 2026 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agre... |
c9f735f03d4c83dc75b6b86fab08518b4c2d0f67668c05dd14bd2a73bbacd57b | Python | 10,097 | 246 | #!/usr/bin/env python
#
# Script to package data for manual correction.
#
# For full help, please run: python package_for_correction.py -h`
#
# Example:
# python package_for_correction.py
# -path-in ~/<your_dataset>/data_processed
# -config config.yml
#
# Authors: Jan Valosek, Sandrine Bédard, Julien ... |
1384bd8cf420ab8b1f03e9b03175380d795d38bba9df9801c29f4df27391a964 | Python | 10,101 | 289 | """Tests for the two session-18 consultation types: experiment designer +
run explainer. The router/provider/audit plumbing is already covered by
`test_llm.py`; these tests focus on the consultation-specific validation
+ happy paths using the FakeLLMProvider.
"""
from __future__ import annotations
import io
from coll... |
7b79bef819514a01d2706b7971052749213261e7d6fe208105f743ac0ae531b8 | Python | 10,104 | 264 | """Test nimare.transforms."""
import re
import nibabel as nib
import numpy as np
import pytest
from nimare import transforms
def test_ImageTransformer(testdata_ibma):
"""Smoke test on transforms.ImageTransformer."""
dset = testdata_ibma
z_files = dset.images["z"].tolist()
z_transformer = transforms.... |
3960831670d107b01b633cc949cf8c00cb5c5439ecce9ff4e3def16de5401593 | Python | 10,105 | 271 | # Copyright 2018-2024 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
9df87a9fee96420adfe5cff2b1e0dd48e4929b3d43fb6ca171b48eb24e7b9696 | Python | 10,116 | 255 | """Operator enforcing constraints by variable transformations."""
from collections.abc import Sequence
import torch
from mrpro.operators.EndomorphOperator import EndomorphOperator, endomorph
def sigmoid(x: torch.Tensor, beta: float = 1.0) -> torch.Tensor:
"""Beta scaled sigmoid function."""
return torch.nn... |
4ccd4c89975d777122308baefa16cde27d673e89dbc61ab42156c6c9ddfecfe3 | Python | 10,122 | 329 | import pytest
from pandas.core.dtypes.missing import array_equivalent
import pandas as pd
# Fixtures
# ========
@pytest.fixture
def df():
"""DataFrame with columns 'L1', 'L2', and 'L3'"""
return pd.DataFrame({"L1": [1, 2, 3], "L2": [11, 12, 13], "L3": ["A", "B", "C"]})
@pytest.fixture(params=[[], ["L1"], ... |
72e6e429a467996d910f8500459a4af639a87e2de0fab29d39a63249078a55de | Python | 10,123 | 219 | # sourcery skip: avoid-builtin-shadow
import argparse
import subprocess
import sys
import os
DASDC_version = '1.0.1'
description_text = "\n".join([
"==========================================================================",
"DASDC: (D)omain (A)daptation (S)weep (D)etection and (C)lassification",
"======... |
49a23aa27ef2dd403089e61fc93fa1f72cd9670574e06fbaa6d894c66b99bc9d | Python | 10,135 | 336 | """
Summary stat helpers for computing and plotting summary statistics.
Note: "real" should alwasy be first, followed by simulated.
Author: Sara Mathieson, Rebecca Riley
Date: 9/27/22
"""
# TODO some of these could be replaced with tskit
# https://tskit.readthedocs.io/en/stable/python-api.html#tskit.TreeSequence
# py... |
1fc6e2a86776ad4dab301e0ff7e96511769e7828f74f873476bc7343db000ddb | Python | 10,136 | 245 | # Copyright 2018-2025 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
a6fff19d712eb162e020d06de20641cda7da44eea5f4328bb1fc1818befacfcb | Python | 10,138 | 225 | # coding=utf-8
# Code from: https://github.com/alafuzof/NeuralynxIO
from __future__ import division
import os
import warnings
import numpy as np
import datetime
HEADER_LENGTH = 16 * 1024 # 16 kilobytes of header
NCS_SAMPLES_PER_RECORD = 512
NCS_RECORD = np.dtype([('TimeStamp', np.uint64), # Cheetah ti... |
ea6e9a281804d637414e39d45c348cce20f59c6eca072c624bd05fdedf3d97f9 | Python | 10,138 | 277 | """ add_supplementary_images.py
Add supplementary images to publishedURL and create an order file
*****************************************************************
WARNING
This program was written for one specific use - to add skeletons
for FlyWire. It is generalized to a... |
4dac23a64518a09b719d7c48cf22f74409daee86151a017f5e7e4f8f8a2fb955 | Python | 10,140 | 313 | from datetime import (
datetime,
timedelta,
)
import operator
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
class TestTimestampComparison:
def test_compare_non_nano_dt64(self):
# don't raise when converting dt64 to Timestamp in __richcmp__
dt = np.date... |
9501da61e56c05f94eb01715da0b3202d60bd89c680b095fd53f14ff14a337dd | Python | 10,140 | 332 | """
Tests for the following offsets:
- YearBegin
- YearEnd
"""
from __future__ import annotations
from datetime import datetime
import numpy as np
import pytest
import pandas as pd
from pandas.tests.tseries.offsets.common import (
assert_is_on_offset,
assert_offset_equal,
)
from pandas.tseries.offsets impo... |
a3bd52ff97cf1952942067d550e5a6a1b6ad2693440aecde7e938e14111c8ed8 | Python | 10,140 | 252 | #!/usr/bin/env python
# coding: utf-8
### Author: federica.magnabosco@mrc-cbu.cam.ac.uk
### Fit decoding model LDvsSD individual ROIs and save accuracy
# Import some relevant packages.
import numpy as np
import pandas as pd
import pickle
from sklearn.pipeline import make_pipeline
from sklearn.preprocessing import S... |
edcd5d6c94bc0b62de94c3f4b30bdad366a3f31e031739b83360385125a37d4e | Python | 10,141 | 324 | """
Wrappers for tools for calculation of evolutionary
couplings from sequence alignments.
Authors:
Thomas A. Hopf
"""
from collections import namedtuple
import re
import pandas as pd
from evcouplings.utils.system import (
run, valid_file, create_prefix_folders,
verify_resources, ResourceError
)
def par... |
bf6e2e33abf097180b0875c9a7502542a735b78d462a0d3610dcd58501c11ef9 | Python | 10,146 | 308 | """Miscellaneous functions used for plotting gradient data"""
import gzip
import math
import os.path as op
import pickle
import nibabel as nib
import numpy as np
import seaborn as sns
from matplotlib import pyplot as plt
from neuromaps.datasets import fetch_fslr
from nilearn import image, masking, plotting
from nilear... |
52e66c1f7495bb9da59d2f83a5ef69b1c7951b2b2f55f04fe825a9caa54188dd | Python | 10,147 | 267 | """Module contains classes and functions for loading and storing moseq data."""
from collections import Counter
from dataclasses import dataclass
from typing import Dict, List, Optional, Union
from typing_extensions import Literal
import numpy as np
from moseq2_viz.model.util import get_syllable_statistics, get_transi... |
87507fa5280732531c4d2bd0823f9cb87bde1064252281b46b8f980192f6bc33 | Python | 10,154 | 301 | import olefile as ofio
import io
from struct import unpack, calcsize
# Assume the .JWS file is packed as little-endian (x86 processors)
# For Jasco SpectraManager 1.5 files
JWS_150_HEADER_FORMAT = "<L126sHLdddlll20xlll20x6i6i6i6i32s32s64s128s32s96s148s32s16s32s32s64sl148x80s596x"
JWS_MAGIC_BYTES = 0x20537E4C
... |
bff46424d6995b48eb787d5702561463ffcce74e42289e7d84b6c2f361e12d03 | Python | 10,161 | 248 | import h5py
import numpy as np
import scipy
from scipy import stats as scipy_stats
import matplotlib
import matplotlib.pyplot as plt
class AnalyzePrf:
"""
Initializes an instance of the AnalyzePrf class.
This class performs advanced analyses on Population Receptive Field (pRF) mapping data ac... |
faf61a8fa0e857be24df83012634b80d85c4b126d3ca1931864907854663b3b8 | Python | 10,163 | 362 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Mar 14 20:43:48 2021
@author: reisertm
"""
import sys
import os
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as npss
import tensorflow as tf
import math
from tensorflow.keras import Model
from tensorflow.keras import layers
... |
274d0feff16353de225b93b2a910004c96c5cb67d1310161ea7878b939633543 | Python | 10,169 | 317 | # Copyright 2018-2025 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
b4b7f190f4aba18ca88dbfa88f792e2ae285bd47ab3ac1910d54239b35c5171b | Python | 10,169 | 220 | import torch
import torch.nn as nn
import torch.nn.functional as F
import math
import numpy as np
torch.set_default_dtype(torch.float64)
class SiLU(nn.Module):
# from https://pytorch.org/docs/stable/_modules/torch/nn/modules/activation.html#SiLU, since it is missing in 1.6.0
def __init__(self, inplace = ... |
593025c0c0f366869c6b791582897cec95b1710bbbc354f835d6426649f4814b | Python | 10,170 | 257 | from __future__ import absolute_import
from __future__ import unicode_literals
from __future__ import print_function
from __future__ import division
import torch
import torch.nn as nn
from torch.autograd import Variable
import torch.nn.functional as F
class LearnedGroupConv(nn.Module):
global_progress = 0.0
... |
9a813b135db73dad5bd05e0feb1c84065e53909af319e0ae8c7d89be90f01b2b | Python | 10,172 | 245 | #!/usr/bin/env python
# coding: utf-8
### Author: federica.magnabosco@mrc-cbu.cam.ac.uk
### Fit decoding model LDvsSD individual ROIs and save accuracy
# Import some relevant packages.
import numpy as np
import pandas as pd
import pickle
from sklearn.pipeline import make_pipeline
from sklearn.preprocessing import S... |
27d036c8bfdafe5a3d0d68408cba31d164a3e4f8783f2ccaf18ba2123b3f5d7f | Python | 10,177 | 264 | import numpy as np
import torch
from .interpolation import interpolate_sparse_data, get_smooth_data
from .HDF5Dataset import HDF5Dataset
import windseer.utils as utils
def load_measurements(config, config_model):
'''
Load the sparse data according to the input settings
Parameters
----------
conf... |
254440aee3f15b739333bc1569f487ca42bc3c57618c5ee4ac8004c569858ba5 | Python | 10,185 | 278 | """Integration tests for the SAM workflow."""
from __future__ import annotations
import numpy as np
import pytest
import scipy.sparse as sp
from anndata import AnnData
from samalg import SAM
from samalg.exceptions import DataNotLoadedError
class TestSAMInitialization:
"""Tests for SAM object initialization."""... |
8351d9dc4c9b52a0909f98c8b68f4f9023410847ec1035429fcec085a6cb5099 | Python | 10,187 | 258 | import numpy
import time
import warnings
from spycon.spycon_result import SpikeConnectivityResult
from itertools import combinations
class SpikeConnectivityInference(object):
"""
Base class for spike connectivity inference. It will infer a fully connected graph.
Args:
params (dict): Dictionary wi... |
73c81eb1451264f53e0d794e2278923dc2ef801ab692e4201a3c972e1a45a9be | Python | 10,188 | 284 | import gzip
import os.path as op
import pickle
from difflib import get_close_matches
from glob import glob
import numpy as np
import pandas as pd
from gradec.fetcher import _fetch_features
from sklearn.feature_extraction.text import TfidfTransformer
def _extract_semantic_similarity(max_feature, ic_df, tfidf_df, freq... |
56fa196d5fca2c86ac62fc299ddf32a6f3af62aad66ce1b5332a685f4cb4dbd7 | Python | 10,190 | 278 | import string
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.core.arrays.sparse import SparseArray
class TestSeriesAccessor:
def test_to_dense(self):
ser = pd.Series([0, 1, 0, 10], dtype="Sparse[int64]")
result = ser.sparse.to_dense()
expect... |
54fb61f06eda08f95147019fc64738d4832d02339400803212e45e32314a03a7 | Python | 10,193 | 234 | # Copyright 2026 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agre... |
caf0bb4e9ba5aa7909e9a6cd11e92b8a2de2b683d217356b45d044d7b66359c2 | Python | 10,195 | 251 | import sys
import numpy as np
import wormdatamodel as wormdm
import wormbrain as wormb
import matplotlib.pyplot as plt
import os
import mistofrutta as mf
import pumpprobe as pp
plot = True
folder = sys.argv[1]
if folder[-1]!="/": folder += "/"
save = "--no-save" not in sys.argv
sig_green = "--signal:green" in sys.arg... |
c48a24b968cf4eb92d2d9a9c4e00bce36dc84bcfffa711f3ae282df0333bd11d | Python | 10,197 | 236 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
#importing required libraries
import torch
import torch.nn as nn
from torch.utils.data import TensorDataset, DataLoader
import numpy as np
from esmologs.ESM2_to_3Di import ESM2_to_3Di, SeqsDataset
import argparse
import sys
import re
from pathlib import Path
import loggin... |
f8fe87014203fbe5b3c0bc1b8db24d2faa3e3d764dabca6b96492a44f3952a5d | Python | 10,208 | 284 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.core.arrays import IntervalArray
@pytest.fixture(
params=[
(pd.Index([0, 2, 4]), pd.Index([1, 3, 5])),
(pd.Index([0.0, 1.0, 2.0]), pd.Index([1.0, 2.0, 3.0])),
(
pd.timedelta_range("0 ... |
01c7aeccd823fa8b32430712736a73ff2fd22eda0baab519997746559a7723d6 | Python | 10,216 | 243 | # Copyright 2026 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agre... |
6b25939e5ce3bacdf5ad5c3a3a1ea0c485219438cb8ebcdd168079e0e6f97eea | Python | 10,221 | 267 | import numpy as np
import pytest
import pandas.util._test_decorators as td
import pandas as pd
from pandas.tests.plotting.common import (
_check_legend_labels,
_check_legend_marker,
_check_text_labels,
)
mpl = pytest.importorskip("matplotlib")
class TestFrameLegend:
@pytest.mark.xfail(
reas... |
6b2fcc06ff8959905cdcebe1a5f35d37ffb14ddfb993e420d937eace5b0064e6 | Python | 10,235 | 274 | # Copyright 2021 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agre... |
dc557e41a7bd1a2ba0d7ce85cdbbede09cb5f0187e7b94cfa58da13b74ff0799 | Python | 10,235 | 323 | """
Copyright (c) 2019 Pedro F. Proenza
"""
import numpy as np
import math as math
def euler2SO3_unreal(pitch, yaw, roll):
"""Convert euler angles in degrees to a rotation matrix using unreal engine order (valid)"""
cos_pitch = np.cos(pitch*np.pi/180)
sin_pitch = np.sin(pitch*np.pi/180)
cos_yaw = np.c... |
21aee167560f6c3dd3312cd6e812b158d6d99eb0997ab6f3ba6cdde5de05b887 | Python | 10,250 | 299 | """
Allows us to read in real data regions randomly, and also use a mask (bed
format) file so we don't use regions that are uncallable.
Author: Sara Mathieson, Rebecca Riley
Date: 9/27/22
"""
# python imports
from collections import defaultdict
import h5py
import numpy as np
from numpy.random import default_rng
import... |
95de5bfefaa6769d50e78f9ae36e93938151c72d23946c7b4801b9af6f600f6a | Python | 10,252 | 256 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Import raw data. Do initial cleaning. Run ICA and remove components correlted with EOG and ECG. Save figures in subj
folder for inspection.
Vinding, M. C., Eriksson, A., Low, C. M. T., Waldthaler, J., Ferreira, D., Ingvar, M., Svenningsson, P., & Lundqvist, D. (2021)... |
b2af31656b169289023b22dce2b2814fb2a43535d8837e1bb499f5efff289487 | Python | 10,255 | 301 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.api.types import is_integer
from pandas.core.arrays import IntegerArray
from pandas.core.arrays.integer import (
Int8Dtype,
Int32Dtype,
Int64Dtype,
)
@pytest.fixture(params=[pd.array, IntegerArray._from_sequence... |
9c93a094bc0c6470c5194dc98ccb6224f2cc618f776ce0ec294ed7086cd1ddf4 | Python | 10,259 | 358 | """
Module for scope operations
"""
from __future__ import annotations
from collections import ChainMap
import datetime
import inspect
from io import StringIO
import itertools
import pprint
import struct
import sys
from typing import (
Any,
TypeVar,
)
import numpy as np
from pandas._libs.tslibs import Times... |
d04f234b298d26994c93db6e4de8fa0fb2e7fb7d357c36105b7c4a3153374b55 | Python | 10,260 | 269 | """Configuration for Scanpy’s Sphinx documentation."""
from __future__ import annotations
import os
import shutil
import sys
from datetime import datetime
from functools import partial
from importlib.metadata import version as get_version
from pathlib import Path
from typing import TYPE_CHECKING
import matplotlib #... |
273d611676cff4f8d6d6e5b1eadcb2469c4e61dc6fdccfc1945fef3a22d3f0d9 | Python | 10,263 | 296 | # Copyright 2024 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agre... |
29722ffa8442c65355601f8622438cd64ce762c576e10d70ac3616e3a4657897 | Python | 10,263 | 287 | import torch
import numpy
import matplotlib.pyplot as plt
from src import bionetwork
from src import plotting
import pandas
from scipy.stats import pearsonr
#import pandas as pd
batchSize = 1
#Load network
networkList, nodeNames, modeOfAction = bionetwork.loadNetwork("data/ToyNetRecurrent-Model.txt")
annotation = pan... |
2145b8f473cb3d62bfba115a4424971e4a3c259870e18919fc46caaa4d576b21 | Python | 10,266 | 328 | import pytest
from pandas.errors import CSSWarning
import pandas._testing as tm
from pandas.io.formats.css import CSSResolver
def assert_resolves(css, props, inherited=None):
resolve = CSSResolver()
actual = resolve(css, inherited=inherited)
assert props == actual
def assert_same_resolution(css1, css... |
9c9142428dd75b7a3ff6469ff84e97f328c654b3da941ab3dca9187e28694b9c | Python | 10,270 | 188 | # MIT License
#
# Copyright 2026 Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, ... |
923717e90197ac58bbf736cb29a75c91cbbd82c9717cb2b5040281836c10d20c | Python | 10,275 | 290 | from datetime import datetime
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.core.algorithms import safe_sort
def equal_contents(arr1, arr2) -> bool:
"""
Checks if the set of unique elements of arr1 and arr2 are equivalent.
"""
return frozenset(arr1) ==... |
75ec13da1ea368003ea1885273a132dd0716e0e4ccf7c00f77eed9e4f287e2de | Python | 10,291 | 295 | #!/usr/bin/env python3
# Copyright 2015 Google, Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless require... |
58f246e515251828a1b95449592341faabd23fedfc3acc319a10806f102e57b6 | Python | 10,292 | 229 |
import os
import shutil
def compare(vcf_file, tool_out_path, compare_type):
print(vcf_file)
gz_vcf = vcf_file + '.gz'
cmd_str = 'bgzip -c {0} > {1}'.format(vcf_file, gz_vcf)
os.system(cmd_str)
cmd_str = 'tabix -p vcf {0}'.format(gz_vcf)
os.system(cmd_str)
if compare_type == 'region':... |
92980d93e398047309d6f55ca2050f96700f10f952a9f5dc5d8199da554e94d8 | Python | 10,293 | 279 | """Audit-log middleware — records every mutating API call.
Spec § 17.4. One append-only row per POST / PATCH / PUT / DELETE against
``/api/v1/*``. Read requests + heartbeats are skipped — they're noisy and
rarely forensically interesting.
Design:
- Middleware runs *after* auth resolution so it can read ``request.sta... |
d4b85c41d35184fa1009b0340d9985f1cec214588376f6c43ae0ff491fa5eeba | Python | 10,301 | 288 | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import numpy as np
import sympy as sym
from scipy import special as sp
from scipy.optimize import brentq
def Jn(r, n):
"""
numerica... |
5aebd53a210c94113a037fc90f55232800b09917fbaa88fc26e61554604884cf | Python | 10,304 | 235 | # -*- coding: utf-8 -*-
import re
import numpy as np
import random
from sdna.sim.core import *
class ErrorSimulation(object):
MUTATION_MODES = ["insertion", "deletion", "mismatch"]
def __init__(self, sequence, seed=None):
"""
Class is used to apply modifications to a sequence.
:pa... |
dcccea30e3d96bbe830627ac98333b7fe6189d56fa33902ad4bf2fafd83e9363 | Python | 10,304 | 260 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
c90b041e07e994d0c8b3f9336632f3ddefa0c9753d57eee8c2d9e86028ed03ac | Python | 10,305 | 290 | """Session-19 tests: failure debugger + deployment reviewer + API keys.
Same fake-LLM-provider test pattern as session 17/18. API-key tests don't
need the LLM; they just exercise the CRUD + hash-on-create invariant.
"""
from __future__ import annotations
from collections.abc import Generator
import pytest
from fast... |
826e77e64d9d8110db6cadc89328be7f0fb0d1eb46d4599a0c8a1eabbbc79e70 | Python | 10,306 | 304 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
class TestDataFrameDiff:
def test_diff_requires_integer(self):
df = pd.DataFrame(np.random.default_rng(2).standard_normal((2, 2)))
with pytest.raises(ValueError, match="periods must be an integer"):
df.d... |
3be30dcf5623be8fa7728014c7adce2081e767603e7770c514f87cff2ef870cd | Python | 10,308 | 242 | """Schema bootstrap — the bridge between SQLite dev and Alembic-managed prod.
`ensure_schema(engine, dev_auto_migrate=True)`:
- If ``alembic_version`` table already exists, assume the operator is running
migrations themselves → no-op.
- Else if ``dev_auto_migrate`` is True (defaults to SQLite dev), call
``alembic... |
703b62010ae84ace0a4bd14a4afa12e5a5187666e62cdf4a78efb827717eab6a | Python | 10,310 | 355 | from __future__ import annotations
from typing import Final
magic: Final = (
b"\x00\x00\x00\x00\x00\x00\x00\x00"
b"\x00\x00\x00\x00\xc2\xea\x81\x60"
b"\xb3\x14\x11\xcf\xbd\x92\x08\x00"
b"\x09\xc7\x31\x8c\x18\x1f\x10\x11"
)
align_1_checker_value: Final = b"3"
align_1_offset: Final = 32
align_1_length:... |
110eb5fea52d2a4b1e91f18730b637cf627cfd0f7786f255ba324becc3388665 | Python | 10,311 | 225 | # Copyright 2026 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agre... |
8b223c250b3992bd74a6d3beef675dcf639f7ed6e5558d62888380fc475ed075 | Python | 10,315 | 324 | # Copyright 2018-2022 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
726b2101174e004dceaae58144adc4c196105ade278a5fd63c87de03a3bf409c | Python | 10,318 | 280 | # -*- coding: utf-8 -*-
# @File name: plot_general_shutter.py
# @Author: Alicia Garrido-Peña
# @Date: 2023-08-09 19:40:58
# @Contact: alicia.garrido@uam.es
# "Copyright (c) 2023 Alicia Garrido-Peña. All Rights Reserved."
# Use of this source code is govern by GPL-3.0 license that
# can be found in the LICENSE file
... |
3d6184a29fbbecf3f2d664a156a68e7b156a462d368586386b9d4b9f04e2a0ed | Python | 10,327 | 282 | #python calcngramprobtoks.py ngramFile textFile
from __future__ import division
import math, sys, os
sys.path.append(os.path.join(os.path.dirname(__file__), '..', '..', 'resource-gcg', 'scripts'))
from model import Model,CondModel
ngramfileix = 1
textfileix = 2
endofsentpunc = ['.','!','?']
#######################... |
21919d274dc0fe6f04d1cbcb177db742260d3fa4d004df396d132c9b0c4ca6b3 | Python | 10,328 | 283 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
7146ff02a3747211270889dbfea8037a74666219d8c531e6100a8d4970a34a77 | Python | 10,339 | 324 | # Copyright 2018-2024 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
cdccd687a6271d3fcd31733af7418f2e129f4d304d53809daec61995b146fcae | Python | 10,339 | 326 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
@pytest.mark.parametrize("align_axis", [0, 1, "index", "columns"])
def test_compare_axis(align_axis):
# GH#30429
df = pd.DataFrame(
{"col1": ["a", "b", "c"], "col2": [1.0, 2.0, np.nan], "col3": [1.0, 2.0, 3.0]},
... |
92f92837928af8a99bae9d519eba200fa5515969a47948f394df5c1ae8d7f9bd | Python | 10,343 | 260 | __author__ = "etseng@pacb.com"
import pdb
"""
For Iso-Phase, selecting loci that has sufficient FL coverage to phase.
INPUT:
-- FLNC (fastq)
-- Unique isoforms and genes (GFF), using PB.X.Y to denote gene vs isoforms relationship
-- FLNC association to isoforms, (.read_stat.txt)
-- Reference genome (fasta... |
ec04d9d91a4c646de54b7c19dbc8bd4580efc827a5daa81ca82703321a282f94 | Python | 10,343 | 104 | #! /usr/bin/env python3
# iss #159 : nhmmer reports overlapping envelopes on reverse strand
#
# A bug in how nhmmer sorts hits on reverse strand led to it reporting
# overlapping envelopes in some situations.
#
# [xref SRE:2019/0531-nhmmer-iss159]
import sys
import os
import subprocess
if len(sys.argv) != 4:
sys... |
139ee92f665f5858da79b9e8a7c4982241e6a637fe00a8acd6f8aae4885b5871 | Python | 10,345 | 312 | from __future__ import annotations
import numbers
from typing import (
TYPE_CHECKING,
Any,
Self,
)
import numpy as np
from pandas._config import is_nan_na
from pandas._libs import (
lib,
missing as libmissing,
)
from pandas.errors import AbstractMethodError
from pandas.util._decorators import ca... |
c4e61b5b4306a687f700629dca4f551802d675a05992daa10731bbf6758f57b8 | Python | 10,347 | 198 | # MIT License
#
# Copyright 2026 Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, ... |
f1e23ff3c455b02464c4c7c23b69efcace7dba8d3538c0da565c6fb19375c18d | Python | 10,347 | 290 | # Copyright 2018-2022 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
11ecd7770e84499272e2ef4a3c7231f22723b8fccd691f789ac0983793687cf7 | Python | 10,349 | 343 | from __future__ import annotations
import enum
import inspect
import re
from contextlib import contextmanager
from dataclasses import dataclass
from functools import cache, cached_property, partial, wraps
from importlib.metadata import distributions, requires, version
from typing import TYPE_CHECKING, Literal, NamedTu... |
51f146e0929ddb46482f297264267e6fa4ff9784ad320237debd45249209036b | Python | 10,350 | 293 | import torch
import numpy
import pandas
import seaborn as sns
from scipy import interpolate
import matplotlib.pyplot as plt
import time
import plotting
from scipy.stats import pearsonr
def plotACondition(X, Y, Yhat, YtestHat, Ytest):
plt.figure()
ax1=plt.subplot(2, 2, 1)
df = pandas.DataFrame.from_dict(num... |
9d5253857bdfa0d62c975fd20c415d518048b3af8e1750a9b203a9220fcc849a | Python | 10,353 | 234 | # %% [markdown]
# # Regularized iterative SENSE reconstruction of 2D golden angle radial data
# Here we use the `~mrpro.algorithms.reconstruction.RegularizedIterativeSENSEReconstruction` class to reconstruct
# undersampled images from 2D radial data.
# %% tags=["hide-cell"] mystnb={"code_prompt_show": "Show download d... |
4553db1b5fad1c8a2df8b79972d352fb7eb0ed5f4b296016ab1ff138bb825d5c | Python | 10,358 | 255 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Tue Apr 21 23:45:29 2020
@author: Mehmood Ali Khan
"""
from sklearn import preprocessing
import pandas as pd
import numpy as np
from keras.layers import LSTM
from keras.layers import Bidirectional
from keras.models import Sequential
from keras.... |
ca4c541b805d247bb8fd0956908f1d4938dfc28da23a78bf6bc92e0cab113fd6 | Python | 10,360 | 283 | from nibabel.affines import apply_affine
import numpy as np
from sklearn.linear_model import LinearRegression
from sklearn.preprocessing import RobustScaler, StandardScaler
import torch
import torch.nn.functional as F
from skimage.measure import label as label_connector
import nibabel as nib
def remove_zero(f_data, v... |
c2dc2bd0cdbcc7d792e277adccb3d7a7c8a1719dd3dae968b6837c6b4035906c | Python | 10,361 | 269 | """Session 40 — phase 5b: drain ``TimeSeriesExperiment.create_model``.
Phase 5a (s39) brought TS into the native dispatcher and gave us
``_fit_state`` parity with the other tasks, but ``create_model`` still
delegated to ``self._legacy.create_model`` for TS. Phase 5b drains it.
What this session ships:
- ``TimeSeries... |
960ec3a3813d99b30b3afcdffa1dbbe9da53e3664a1f3efd871d96305844c121 | Python | 10,372 | 274 | # Copyright (c) 2018-2023, NVIDIA Corporation
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of condit... |
853061a01608dd28190728f11468258f349e019a4d2f822a48fd496d7cc05fad | Python | 10,373 | 260 | import os
import numpy as np
import logging
import glob
from .gridscalars import GridScalars, saveImage
from .diffeo import DiffeoParam, Diffeomorphism, Kernel
from skimage.transform import resize as imresize, AffineTransform, EuclideanTransform, warp
from .affineBasis import AffineBasis
from scipy.ndimage.interpolatio... |
c5cdacfe56d7c169940ef57b7887aead89158c5f5445df8d6b14ebbeab41e4af | Python | 10,373 | 271 | """
Tests that work on both the Python and C engines but do not have a
specific classification into the other test modules.
"""
from io import StringIO
import numpy as np
import pytest
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._testing as tm
skip_pyarrow = pytest.mark.usefixtures("... |
4b90afc94d28de04645d148630b8395fb5ed0d87b3978a9e4a6d270bd755c2c7 | Python | 10,377 | 297 | #!/usr/bin/env python3
import json
import errno
import shutil
import pathlib
import os
import sys
import re
import nibabel as nib
import os.path as op
ANAT_T1W = "58c33bcee13a50849b25879a"
ANAT_T2W = "594c0325fa1d2e5a1f0beda5"
DWI = "58c33c5fe13a50849b25879b"
FUNC_TASK = "59b685a08e5d38b0b331ddc5"
FUNC_REGRESSORS = "... |
dc4fa660a570302a164f04f60d633b2a31770ee6c052abf0ae2608994560af39 | Python | 10,377 | 363 | import numpy as np
from pandas import (
Categorical,
Index,
NaT,
Series,
date_range,
)
class IsIn:
params = [
"int64",
"uint64",
"object",
"Int64",
"boolean",
"bool",
"datetime64[ns]",
"category[object]",
"category[int]",... |
32e55b54b7aed990ba9a86644befb94a8e73c4bd8b322ecd4e36efe6f2b57fca | Python | 10,378 | 239 | # Copyright (c) 2018-2023, NVIDIA Corporation
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of condit... |
2d6bf23cbf42ea4bd0fb57db9f0a02568d07004fde93580931ea7170faed51ab | Python | 10,384 | 231 | import re
from collections import Counter
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem.Descriptors import HeavyAtomCount
from rdkit.Chem.Scaffolds import MurckoScaffold
from rdkit.Chem import rdRGroupDecomposition as rdRGD
from rdkit.Chem.BRICS import FindBRICSBonds,BreakBRICSBonds
import ast
i... |
c21523c68eb0c3a59c5e7c652403dbab59cbaacc00a13b7d64edbbcea1d2f4e7 | Python | 10,391 | 224 | import io
import nibabel.freesurfer.io as fs
from PyQt5 import QtWidgets, QtCore
import vtk
from vtkmodules.qt.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
import numpy as np
class Hemisphere(QtWidgets.QWidget):
sgn = QtCore.pyqtSignal(dict)
camera_updated = QtCore.pyqtSignal(vtk.vtkCamera)
... |
30356387c60c1e4fac022598db86fccbc7da7cd0961dc00c065970235bdcfbdd | Python | 10,395 | 230 | import argparse
import os
import ete3
import pandas as pd
from ete3 import NCBITaxa
def get_args():
"""
Get arguments from command line with argparse.
"""
parser = argparse.ArgumentParser(
prog='Convert_metaphlan3_mpa_to_kreport.py',
description="""Convert a MetaPhlAn3 mpa file into kre... |
b09e219f9d3ea98db7262ed19ec7611fa132f4f577f6163d2f9f55c64dd88d2b | Python | 10,400 | 414 | #funcsboot.py
from placerg.funcs import *
from placerg.funcsrg import *
from placerg.funcsall import *
from placerg.objects import *
from scipy.optimize import curve_fit
def bootfunc(a, env):
rate=[]
coeff=[]
eigspec=[]
var=[]
psil=[]
actmom=[]
autocorr=[]
tau=[]
... |
4fe91187367a8beee6e8426cd0d41377efb4c2e5efe4a057be477ac02b9b3fac | Python | 10,401 | 287 | """Template view."""
# -----------------------------------------------------------------------------
# Imports
# -----------------------------------------------------------------------------
import logging
import numpy as np
from phylib.io.array import _index_of
from phylib.utils import Bunch, emit
from phy.plot i... |
4fad022a8ae977a1f0086d152fc16caf08522bf31e78a78b73693853c61c57a8 | Python | 10,402 | 320 | import numpy as np
import torchvision.utils as vutils
import torch, random
import torch.nn.functional as F
# print arguments
def print_args(args):
print("################################ args ################################")
for k, v in args.__dict__.items():
print("{0: <10}\t{1: <30}\t{2: <20}".f... |
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